Many thousands of years ago, a sheet of ice plowed slowly southward up the valley of the old Cayuga River. Then, as the glacier slowly melted back, it impounded a vast system of lakes along its southern boundary. At the north end of Cayuga Lake and on the old bed of one of these fossil lakes, there developed a vast system of marshes through which the Seneca and Clyde Rivers meandered. The historic Montezuma Marshes once extended north for 12 miles, and was up to 8 miles wide. It was one of the most productive marshes in North America.

No one knows when man first met wildfowl in these marshes, but archeological evidence indicates that the earliest known inhabitants were Algonquin Indians. After the Algonquins disappeared, Cayugas of the Iroquois tribe occupied the land. Records of the Jesuit missionaries among the Cayuga Indians mention that the sunlight over the marshes was actually shut off by the clouds of ducks and geese, and the woods abounded with deer.

The name "Montezuma" was first used in 1806 by Dr. Peter Clark. Dr. Clark, a physician from New York City, came to the area because of his interest in the salt deposits which were recently discovered underneath the lakes and marshes. He built a large, by 1808 standards, 12-room house atop a drumlin with a commanding view of the surrounding vast marshes. Dr. Clark, apparently a cosmopolitan traveler for that era, compared his hilltop home with the palace of the Aztec Emperor Montezuma in Mexico City. His home, the marshes, the village, and eventually the refuge all acquired the name.

Until the 19th century, there were no drastic changes in the marshes. With the development of the Erie Canal, it was inevitable that feeder canals from Seneca and Cayuga Lakes would in time link these lakes with the main line. With canal construction, there arose the possibility of draining the marshes. As early as April 5, 1824, an act was passed relative to the draining of the Cayuga Marshes.

Work on the canal system was begun in 1826; in 1828 boats passed from Geneva to the Erie Canal at Montezuma. The Erie Canal did not greatly affect the marshes because there was no dam at the north end of Cayuga Lake, and the Seneca River still flowed directly from the lake into the marshes.

The latter part of the 19th century and the first decade of the 20th was the golden era of waterfowl hunting on the marshes. A great variety of species was taken, but American black duck and northern pintail were among the most common; mallard, wood duck, widgeon and teal were also often found in the hunters bag. Among diving ducks, redhead, scaup, and canvasback were most common. Canada geese were seldom shot on the marshes although large flocks were seen passing overhead.

This type of hunting could not last forever. With unregulated hunting and a nationwide loss of habitat, the continental populations of waterfowl began to dwindle. Shortly thereafter the daily bag limit came into being. The golden era of waterfowling came to an abrupt end in central New York State in 1910 by the construction of the Seneca and Cayuga extensions (Cayuga-Seneca Canal) of the New York State Barge Canal. A lock was built at the north end of Cayuga Lake and a dam was constructed at the outlet of the lake. This effectively lowered the level of the Seneca River by eight to ten feet and the waters drained from the marshes. The meandering rivers were straightened and deepened, thereby creating additional drainage-ways.

In 1937 the Bureau of Biological Survey (precursor to the U.S. Fish and Wildlife Service) purchased more than 2,000 acres of the former marsh. Montezuma Migratory Bird Refuge (now Montezuma National Wildlife Refuge) was established in 1938 to provide resting, nesting, and feeding habitat for waterfowl and other migratory birds. The Civilian Conservation Corps began work on a series of low dikes which would hold water and restore part of the marsh habitat that had once existed. The work progressed slowly; the first refuge manager (Merton Radway 1938-49) faced breakdown of machinery and loss labor; spring floods threatened the newly constructed dikes. However, by 1943, he had great satisfaction in reporting that the newly-created pool had filled and great numbers of waterfowl where using the refuge. Main Pool was created first followed by Tschache Pool. With the exception of May's Point Pool, the other, smaller pools were created after 1945.